Sun Oct 9 08:58:10 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:58:10 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5931 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4855230 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 0.4855230 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.014041 assigned positive charge : 891.7932 centred at (gu) : 90.24057 89.22654 90.86098 assigned negative charge : -890.7870 centred at (gu) : 90.19086 89.25626 91.01124 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8824 nv = 96 ne = 84 npr = 118380 no. pairs analyzed = 118380 no. exposed pairs = 7487 no. arc points = 51428 no. surface atoms = 2505 nbur = 3426 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 288 mr = 4513 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3900000 number of dielectric boundary points 4598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4896 ## 813 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2565131E-10 -1.9761379E-10 midg,1,midg; midg,igrid,midg 4.5505183E-11 -2.0573794E-11 1,midg,midg; igrid,midg,midg -4.3678058E-11 6.1331232E-11 gauss-seidel spectral radius is 0.9783996 estimated iterations to convergence 56 setup time was (sec) 0.5700000 now iterating at: 08:58:11 rms-change max change #iterations 5.9131179E-02 8.303352 at 10iterations 3.4257760E-03 0.5486603 at 20iterations 5.4892513E-04 0.1198654 at 30iterations 1.5622833E-04 3.5108566E-02 at 40iterations 4.8884627E-05 1.0667801E-02 at 50iterations finished qdiffx linear iterations at : 08:58:14 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.8884627E-05 1.0667801E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:58:14 3.555u 0.174s 0:04.01 92.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:58:14 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5931 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.456569 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 1.456569 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.014041 assigned positive charge : 891.7932 centred at (gu) : 90.71967 87.67851 92.58113 assigned negative charge : -890.7870 centred at (gu) : 90.57221 87.76849 93.03362 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 101382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 27757 mr = 69632 m= 2091 mr = 17922 m= 34 mr = 793 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1349 time to turn everything in is 0.4800000 number of dielectric boundary points 42915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 845 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 42454 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.4855230 object centre at (A) : 47.78300 53.11350 31.56350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3109484E-02 -3.4745079E-02 midg,1,midg; midg,igrid,midg 2.6930820E-03 -8.2137939E-03 1,midg,midg; igrid,midg,midg 1.7281916E-03 6.2076570E-03 gauss-seidel spectral radius is 0.9979992 estimated iterations to convergence 178 setup time was (sec) 0.7000000 now iterating at: 08:58:15 rms-change max change #iterations 3.864327 175.8168 at 10iterations 1.538968 51.37303 at 20iterations 0.6157645 18.84165 at 30iterations 0.2461606 7.077772 at 40iterations 9.8497987E-02 2.896650 at 50iterations 3.9495010E-02 1.212406 at 60iterations 1.5915995E-02 0.5602684 at 70iterations 6.4334511E-03 0.1968536 at 80iterations 2.6278300E-03 0.1027527 at 90iterations 1.1125031E-03 3.9472580E-02 at 100iterations 4.9821229E-04 1.8966675E-02 at 110iterations 2.4743730E-04 1.1098862E-02 at 120iterations finished qdiffx linear iterations at : 08:58:22 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.4743730E-04 1.1098862E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 08:58:23 7.885u 0.199s 0:08.35 96.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 08:58:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5931 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.184853 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 14.91900 80.64700 ymin,ymax (A): 20.53100 85.69600 zmin,zma (A): -5.098000 68.22500 x,y,z range (A): 65.72800 65.16500 73.32300 scale (grids/A): 2.184853 object centre (A): 47.78300 53.11350 31.56350 number of atom coordinates read : 5931 total number of charged atoms : 5763 net assigned charge : 1.014041 assigned positive charge : 891.7932 centred at (gu) : 91.07914 86.51723 93.87148 assigned negative charge : -890.7870 centred at (gu) : 90.85822 86.65279 94.55040 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 236091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 102435 mr = 171134 m= 23355 mr = 78779 m= 2714 mr = 16355 m= 99 mr = 1516 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 4716 time to turn everything in is 1.170000 number of dielectric boundary points 96885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 45880 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.456569 object centre at (A) : 47.78300 53.11350 31.56350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5441567 -0.9663318 midg,1,midg; midg,igrid,midg 9.9770665E-02 -0.1730660 1,midg,midg; igrid,midg,midg 3.8803354E-02 8.1107311E-02 gauss-seidel spectral radius is 0.9991623 estimated iterations to convergence 273 setup time was (sec) 1.420000 now iterating at: 08:58:25 rms-change max change #iterations 10.81854 302.5132 at 10iterations 6.225611 143.5956 at 20iterations 3.567053 80.29276 at 30iterations 2.029742 48.32983 at 40iterations 1.153997 22.04460 at 50iterations 0.6507230 13.72398 at 60iterations 0.3681163 8.033695 at 70iterations 0.2069497 4.694351 at 80iterations 0.1163767 2.629692 at 90iterations 6.5164804E-02 1.218975 at 100iterations 3.6534976E-02 0.6930542 at 110iterations 2.0488897E-02 0.3715277 at 120iterations 1.1479875E-02 0.2046967 at 130iterations 6.4251618E-03 0.1123691 at 140iterations 3.6026335E-03 6.3842773E-02 at 150iterations 2.0293011E-03 3.8326263E-02 at 160iterations 1.1478759E-03 2.3338318E-02 at 170iterations 6.5848604E-04 1.2285233E-02 at 180iterations finished qdiffx linear iterations at : 08:58:36 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 6.5848604E-04 1.2285233E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 08:58:37 13.434u 0.220s 0:13.94 97.9% 0+0k 0+0io 0pf+0w